9KKH | pdb_00009kkh

High resolution structure of Ferredoxin-NADP+ reductase from maize root - Reduced form, low X-ray dose

• PDB DOI: https://doi.org/10.2210/pdb9KKH/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Zea mays
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-11-13 Released: 2025-01-29 
• Deposition Author(s): Uenaka, M., Ohnishi, Y., Tanaka, H., Kurisu, G.
• Funding Organization(s): Japan Science and Technology

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 
  0.172 (Depositor), 0.171 (DCC) 
• R-Value Work: 
  0.143 (Depositor), 0.143 (DCC) 
• R-Value Observed: 
  0.143 (Depositor) 

Starting Model: experimental

Literature

Redox-dependent hydrogen-bond network rearrangement of ferredoxin-NADP + reductase revealed by high-resolution X-ray and neutron crystallography.

Uenaka, M., Ohnishi, Y., Ise, A., Yu, J., Yano, N., Kusaka, K., Tanaka, H., Kurisu, G.

(2025) Acta Crystallogr F Struct Biol Commun 81: 73-84

• PubMed: 39913263 
• DOI: https://doi.org/10.1107/S2053230X25000524
• Primary Citation Related Structures: 
  9KK7, 9KKC, 9KKG, 9KKH, 9L8G


• PubMed Abstract: 
  

  High-resolution X-ray and neutron crystallography were employed to elucidate redox-dependent structural changes in ferredoxin-NADP ⁺ reductase (FNR) from maize. This study focused on the rearrangement of hydrogen-bond networks upon FAD reduction. The X-ray structures of wild-type FNR in oxidized and reduced states were refined to 1.15 and 1.10 Å resolution, respectively, revealing no large structural changes in the main-chain backbones. Neutron crystallography provided complementary insights, confirming protonation at N1 and N5 of the isoalloxazine ring and visualizing hydrogen bonds that were undetectable by X-ray analysis. These findings illuminate the dynamic reorganization of water-mediated hydrogen-bond networks during redox transitions, which may underpin the redox-dependent modulation of partner binding by FNR. This integrated structural approach highlights the synergistic use of X-ray and neutron crystallography in studying redox-active proteins.

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Organizational Affiliation: 
• Protein Crystallography Laboratory, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.
Structural Biology Division, Japan Synchrotron Radiation Research Institute, Hyogo 679-5198, Japan.
Neutron Industrial Application Promotion Center, Comprehensive Research Organization for Science and Society, Tokai, Ibaraki 319-1106, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 36.22 kDa 
• Atom Count: 3,462 
• Modeled Residue Count: 309 
• Deposited Residue Count: 311 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferredoxin--NADP reductase, chloroplastic	A	311	Zea mays	Mutation(s): 0  Gene Names: 542713, ZEAMMB73_Zm00001d034345 EC: 1.18.1.2
UniProt
Find proteins for B4G043 (Zea mays) Explore B4G043  Go to UniProtKB:  B4G043

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FDA (Subject of Investigation/LOI)	D [auth A]	DIHYDROFLAVINE-ADENINE DINUCLEOTIDE C27 H35 N9 O15 P2 YPZRHBJKEMOYQH-UYBVJOGSSA-N
MES	B [auth A], C [auth A], E [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free:  0.172 (Depositor), 0.171 (DCC) 
• R-Value Work:  0.143 (Depositor), 0.143 (DCC) 
• R-Value Observed: 0.143 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.08	α = 90
b = 59.08	β = 90
c = 186.9	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-01-29 
Deposition Author(s): Uenaka, M., Ohnishi, Y., Tanaka, H., Kurisu, G.

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Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	JPMJSP2138

Revision History  

• Version 1.0: 2025-01-29
  Type: Initial release
  
• Version 1.1: 2025-02-19
  Changes: Database references
• Version 1.2: 2025-03-12
  Changes: Database references